A cubature Kalman filter approach for inferring gene regulatory networks using time series data

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

A novel technique for the inference of gene regulatory networks is proposed which utilizes cubature Kalman filter (CKF). The gene network is modeled using the state-space approach. A non-linear model for the evolution of gene expression is considered and the microarray data is assumed to follow a linear Gaussian model. CKF is used to estimate the hidden states as well as the unknown static parameters of the model. These parameters provide an insight into the regulatory relations among the genes. The proposed algorithm delievers superior performance than the linearization based extended Kalman filter (EKF) for synthetic as well as real world biological data.

Original languageEnglish
Title of host publicationProceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
Pages25-28
Number of pages4
Publication statusPublished - 2011
Externally publishedYes
Event2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 - San Antonio, TX, United States
Duration: 4 Dec 20116 Dec 2011

Other

Other2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
CountryUnited States
CitySan Antonio, TX
Period4/12/116/12/11

Fingerprint

Gene Regulatory Networks
Kalman filters
Time series
Genes
Nonlinear Dynamics
Linear Models
Extended Kalman filters
Microarrays
Gene Expression
Linearization
Gene expression

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Signal Processing
  • Biomedical Engineering

Cite this

Noor, A., Serpedin, E., Nounou, M., & Nounou, H. (2011). A cubature Kalman filter approach for inferring gene regulatory networks using time series data. In Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 (pp. 25-28). [6169432]

A cubature Kalman filter approach for inferring gene regulatory networks using time series data. / Noor, Amina; Serpedin, Erchin; Nounou, Mohamed; Nounou, Hazem.

Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. p. 25-28 6169432.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Noor, A, Serpedin, E, Nounou, M & Nounou, H 2011, A cubature Kalman filter approach for inferring gene regulatory networks using time series data. in Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11., 6169432, pp. 25-28, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11, San Antonio, TX, United States, 4/12/11.
Noor A, Serpedin E, Nounou M, Nounou H. A cubature Kalman filter approach for inferring gene regulatory networks using time series data. In Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. p. 25-28. 6169432
Noor, Amina ; Serpedin, Erchin ; Nounou, Mohamed ; Nounou, Hazem. / A cubature Kalman filter approach for inferring gene regulatory networks using time series data. Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. pp. 25-28
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